all?
# no facet
plot_ordination(Fun_wholecommunity, Fun_wholecommunity.k3.ord, color = "Gradient") +
geom_text(mapping = aes(label = Site_Grass), size = 4, vjust = 1.5) +
scale_color_manual(values = fun_grad_cols_n3
# ,name="Grass Host"
) +
geom_point(size = 3, alpha = 0.9) +
labs(y="") +
ggtitle("", subtitle = "ITS - k=3") +
theme_bw() +
theme(legend.position="right",
axis.text.x = element_text(color="black", size=12),
axis.text.y = element_text(color="black", size=12),
axis.title.x = element_text(color="black", size=14),
axis.title.y = element_text(color="black", size=14),
plot.background = element_blank(),panel.border = element_rect(colour = "black", fill=NA, linewidth=.75),
panel.grid.major = element_blank(),panel.grid.minor = element_blank(),panel.background = element_blank())
plot_ordination(Fun_wholecommunity, Fun_wholecommunity.k3.ord, color = "Bin") +
geom_text(mapping = aes(label = Site_Grass), size = 4, vjust = 1.5) +
scale_color_manual(values = fun_bin_cols_n5
# ,name="Grass Host"
) +
geom_point(size = 3, alpha = 0.9) +
labs(y="") +
ggtitle("", subtitle = "ITS - k=3") +
theme_bw() +
theme(legend.position="right",
axis.text.x = element_text(color="black", size=12),
axis.text.y = element_text(color="black", size=12),
axis.title.x = element_text(color="black", size=14),
axis.title.y = element_text(color="black", size=14),
plot.background = element_blank(),panel.border = element_rect(colour = "black", fill=NA, linewidth=.75),
panel.grid.major = element_blank(),panel.grid.minor = element_blank(),panel.background = element_blank())
plot_ordination(Fun_wholecommunity, Fun_wholecommunity.k3.ord, color = "Grass") +
geom_text(mapping = aes(label = Site_Grass), size = 4, vjust = 1.5) +
scale_color_manual(values = fun_grass_cols
# ,name="Grass Host"
) +
geom_point(size = 3, alpha = 0.9) +
labs(y="") +
ggtitle("", subtitle = "ITS - k=3") +
theme_bw() +
theme(legend.position="right",
axis.text.x = element_text(color="black", size=12),
axis.text.y = element_text(color="black", size=12),
axis.title.x = element_text(color="black", size=14),
axis.title.y = element_text(color="black", size=14),
plot.background = element_blank(),panel.border = element_rect(colour = "black", fill=NA, linewidth=.75),
panel.grid.major = element_blank(),panel.grid.minor = element_blank(),panel.background = element_blank())
# facet Grass
plot_ordination(Fun_wholecommunity, Fun_wholecommunity.k3.ord, color = "Gradient") +
geom_text(mapping = aes(label = Site_Grass), size = 4.5, vjust = 1.5) +
scale_color_manual(values = fun_grad_cols_n3
# ,name="Grass Host"
) +
geom_point(size = 3, alpha = 0.9) +
facet_wrap(.~Grass, scales = "free") +
labs(y="") +
ggtitle("", subtitle = "ITS - k=3") +
theme_bw() +
theme(legend.position="right",
axis.text.x = element_text(color="black", size=12),
axis.text.y = element_text(color="black", size=12),
axis.title.x = element_text(color="black", size=14),
axis.title.y = element_text(color="black", size=14),
plot.background = element_blank(),panel.border = element_rect(colour = "black", fill=NA, linewidth=.75),
panel.grid.major = element_blank(),panel.grid.minor = element_blank(),panel.background = element_blank())
plot_ordination(Fun_wholecommunity, Fun_wholecommunity.k3.ord, color = "Bin") +
geom_text(mapping = aes(label = Site_Grass), size = 4.5, vjust = 1.5) +
scale_color_manual(values = fun_bin_cols_n5
# ,name="Grass Host"
) +
geom_point(size = 4, alpha = 0.9) +
# scale_size_manual(values = c(3,6)) +
facet_wrap(.~Grass, scales = "free") +
labs(y="") +
ggtitle("", subtitle = "ITS - k=3") +
theme_bw() + #default is 11
theme(legend.position="right",
axis.text.x = element_text(color="black", size=12),
axis.text.y = element_text(color="black", size=12),
axis.title.x = element_text(color="black", size=14),
axis.title.y = element_text(color="black", size=14),
plot.background = element_blank(),panel.border = element_rect(colour = "black", fill=NA, linewidth=.75),
panel.grid.major = element_blank(),panel.grid.minor = element_blank(),panel.background = element_blank())
# facet Bin
plot_ordination(Fun_wholecommunity, Fun_wholecommunity.k3.ord, color = "Grass") +
geom_text(mapping = aes(label = Site), size = 4.5, vjust = 1.5) +
scale_color_manual(values = fun_grass_cols
# ,name="Grass Host"
) +
geom_point(size = 3, alpha = 0.9) +
facet_wrap(.~Bin, scales = "free") +
labs(y="") +
ggtitle("", subtitle = "ITS - k=3") +
theme_bw() +
theme(legend.position="right",
axis.text.x = element_text(color="black", size=12),
axis.text.y = element_text(color="black", size=12),
axis.title.x = element_text(color="black", size=14),
axis.title.y = element_text(color="black", size=14),
plot.background = element_blank(),panel.border = element_rect(colour = "black", fill=NA, linewidth=.75),
panel.grid.major = element_blank(),panel.grid.minor = element_blank(),panel.background = element_blank())
# facet Bin*Gradient
plot_ordination(Fun_wholecommunity, Fun_wholecommunity.k3.ord, color = "Grass") +
geom_text(mapping = aes(label = Site), size = 4.5, vjust = 1.5) +
scale_color_manual(values = fun_grass_cols
# ,name="Grass Host"
) +
geom_point(size = 3, alpha = 0.9) +
facet_wrap(.~Bin:Gradient) +
labs(y="") +
ggtitle("", subtitle = "ITS - k=3, scales=fixed") +
theme_bw() +
theme(legend.position="right",
axis.text.x = element_text(color="black", size=12),
axis.text.y = element_text(color="black", size=12),
axis.title.x = element_text(color="black", size=14),
axis.title.y = element_text(color="black", size=14),
plot.background = element_blank(),panel.border = element_rect(colour = "black", fill=NA, linewidth=.75),
panel.grid.major = element_blank(),panel.grid.minor = element_blank(),panel.background = element_blank())
plot_ordination(Fun_wholecommunity, Fun_wholecommunity.k3.ord, color = "Grass") +
geom_text(mapping = aes(label = Site), size = 4, vjust = 1.5) +
scale_color_manual(values = fun_grass_cols
# ,name="Grass Host"
) +
geom_point(size = 3, alpha = 0.9) +
facet_wrap(.~Bin:Gradient, scales = "free") +
labs(y="") +
ggtitle("", subtitle = "ITS - k=3, scales=free") +
theme_bw() +
theme(legend.position="right",
axis.text.x = element_text(color="black", size=12),
axis.text.y = element_text(color="black", size=12),
axis.title.x = element_text(color="black", size=14),
axis.title.y = element_text(color="black", size=14),
plot.background = element_blank(),panel.border = element_rect(colour = "black", fill=NA, linewidth=.75),
panel.grid.major = element_blank(),panel.grid.minor = element_blank(),panel.background = element_blank())
adonis2(phyloseq::distance(Fun_wholecommunity, method="bray") ~ Site*Grass,
data = (as(sample_data(Fun_wholecommunity), "data.frame")))
anosim(phyloseq::distance(Fun_wholecommunity, method="bray"),
(as(sample_data(Fun_wholecommunity), "data.frame"))$Site, permutations = 1000
)
anosim(BC.dist, meta$AgeGroup, permutations = 1000)
long
plot_ordination(Fun_wholecommunity, Fun_wholecommunity.k3.ord, color = "Gradient", label = "Grass") +
scale_color_manual(values = fun_grad_cols_n3
# ,name="Grass Host"
) +
geom_point(size = 3, alpha = 0.9) +
labs(y="") +
ggtitle("", subtitle = "ITS - k=3") +
theme_bw() +
theme(legend.position="right",
axis.text.x = element_text(color="black", size=12),
axis.text.y = element_text(color="black", size=12),
axis.title.x = element_text(color="black", size=14),
axis.title.y = element_text(color="black", size=14),
plot.background = element_blank(),panel.border = element_rect(colour = "black", fill=NA, linewidth=.75),
panel.grid.major = element_blank(),panel.grid.minor = element_blank(),panel.background = element_blank())
plot_ordination(Fun_wholecommunity, Fun_wholecommunity.k5.ord, color = "Gradient", label = "Grass") +
scale_color_manual(values = fun_grad_cols_n3
# ,name="Grass Host"
) +
geom_point(size = 3, alpha = 0.9) +
labs(y="") +
ggtitle("", subtitle = "ITS - k=5") +
theme_bw() +
theme(legend.position="right",
axis.text.x = element_text(color="black", size=12),
axis.text.y = element_text(color="black", size=12),
axis.title.x = element_text(color="black", size=14),
axis.title.y = element_text(color="black", size=14),
plot.background = element_blank(),panel.border = element_rect(colour = "black", fill=NA, linewidth=.75),
panel.grid.major = element_blank(),panel.grid.minor = element_blank(),panel.background = element_blank())
plot_ordination(Fun_wholecommunity, Fun_wholecommunity.k3.ord, color = "Gradient", label = "Site") +
scale_color_manual(values = fun_grad_cols_n3
# ,name="Grass Host"
) +
geom_point(size = 3, alpha = 0.9) +
facet_wrap(.~Grass) +
labs(y="") +
ggtitle("", subtitle = "ITS - k=3") +
theme_bw() +
theme(legend.position="right",
axis.text.x = element_text(color="black", size=12),
axis.text.y = element_text(color="black", size=12),
axis.title.x = element_text(color="black", size=14),
axis.title.y = element_text(color="black", size=14),
plot.background = element_blank(),panel.border = element_rect(colour = "black", fill=NA, linewidth=.75),
panel.grid.major = element_blank(),panel.grid.minor = element_blank(),panel.background = element_blank())
plot_ordination(Fun_wholecommunity, Fun_wholecommunity.k5.ord, color = "Gradient", label = "Site") +
scale_color_manual(values = fun_grad_cols_n3
# ,name="Grass Host"
) +
geom_point(size = 3, alpha = 0.9) +
facet_wrap(.~Grass) +
labs(y="") +
ggtitle("", subtitle = "ITS - k=5") +
theme_bw() +
theme(legend.position="right",
axis.text.x = element_text(color="black", size=12),
axis.text.y = element_text(color="black", size=12),
axis.title.x = element_text(color="black", size=14),
axis.title.y = element_text(color="black", size=14),
plot.background = element_blank(),panel.border = element_rect(colour = "black", fill=NA, linewidth=.75),
panel.grid.major = element_blank(),panel.grid.minor = element_blank(),panel.background = element_blank())
lat
plot_ordination(Fun_wholecommunity, Fun_wholecommunity.k3.ord, color = "Bin", label = "Grass") +
scale_color_manual(values = fun_bin_cols_n5
# ,name="Grass Host"
) +
geom_point(size = 3, alpha = 0.9) +
labs(y="") +
ggtitle("", subtitle = "ITS - k=3") +
theme_bw() +
theme(legend.position="right",
axis.text.x = element_text(color="black", size=12),
axis.text.y = element_text(color="black", size=12),
axis.title.x = element_text(color="black", size=14),
axis.title.y = element_text(color="black", size=14),
plot.background = element_blank(),panel.border = element_rect(colour = "black", fill=NA, linewidth=.75),
panel.grid.major = element_blank(),panel.grid.minor = element_blank(),panel.background = element_blank())
plot_ordination(Fun_wholecommunity, Fun_wholecommunity.k5.ord, color = "Bin", label = "Grass") +
scale_color_manual(values = fun_bin_cols_n5
# ,name="Grass Host"
) +
geom_point(size = 3, alpha = 0.9) +
labs(y="") +
ggtitle("", subtitle = "ITS - k=5") +
theme_bw() +
theme(legend.position="right",
axis.text.x = element_text(color="black", size=12),
axis.text.y = element_text(color="black", size=12),
axis.title.x = element_text(color="black", size=14),
axis.title.y = element_text(color="black", size=14),
plot.background = element_blank(),panel.border = element_rect(colour = "black", fill=NA, linewidth=.75),
panel.grid.major = element_blank(),panel.grid.minor = element_blank(),panel.background = element_blank())
plot_ordination(Fun_wholecommunity, Fun_wholecommunity.k3.ord, color = "Bin") +
geom_text(mapping = aes(label = Site), size = 5, vjust = 1.5) +
scale_color_manual(values = fun_bin_cols_n5
# ,name="Grass Host"
) +
geom_point(size = 4, alpha = 0.9) +
# scale_size_manual(values = c(3,6)) +
facet_wrap(.~Grass, scales = "free") +
labs(y="") +
ggtitle("", subtitle = "ITS - k=3") +
theme_bw() + #default is 11
theme(legend.position="right",
axis.text.x = element_text(color="black", size=12),
axis.text.y = element_text(color="black", size=12),
axis.title.x = element_text(color="black", size=14),
axis.title.y = element_text(color="black", size=14),
plot.background = element_blank(),panel.border = element_rect(colour = "black", fill=NA, linewidth=.75),
panel.grid.major = element_blank(),panel.grid.minor = element_blank(),panel.background = element_blank())
plot_ordination(Fun_wholecommunity, Fun_wholecommunity.k5.ord, color = "Bin") +
geom_text(mapping = aes(label = Site), size = 5, vjust = 1.5) +
scale_color_manual(values = fun_bin_cols_n5
# ,name="Grass Host"
) +
geom_point(size = 4, alpha = 0.9) +
facet_wrap(.~Grass, scales = "free") +
labs(y="") +
ggtitle("", subtitle = "ITS - k=5") +
theme_bw() + #default is 11
theme(legend.position="right",
axis.text.x = element_text(color="black", size=12),
axis.text.y = element_text(color="black", size=12),
axis.title.x = element_text(color="black", size=14),
axis.title.y = element_text(color="black", size=14),
plot.background = element_blank(),panel.border = element_rect(colour = "black", fill=NA, linewidth=.75),
panel.grid.major = element_blank(),panel.grid.minor = element_blank(),panel.background = element_blank())